Heat resistance in extended-spectrum beta-lactamase-producing Escherichia coli may favor environmental survival in a hospital setting

Methods for studying microbial acid stress responses: from molecules to populations

The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.

Methods for Screening and Isolating Extremely Heat-Resistant Escherichia coli from Meat Sources

Meat animals harbor diverse E. coli populations in their digestive tracts and can serve as sources of pathogenic E. coli. The consumption of meat and produce contaminated with virulent E. coli from animal sources is associated with human illnesses and outbreaks. Heat treatment is an antimicrobial intervention that is commonly used during meat processing to ensure effective reductions in microbial load. Extreme heat resistance (XHR) has been reported among meat-borne E. coli and is mainly attributed to an ~15-19 kb genetic element known as the transmissible locus of stress tolerance (tLST). XHR E. coli can resist treatments used during meat processing and cooking. Therefore, the detection of heat-resistant E. coli is important for devising effective control measures to prevent meat spoilage and ensure meat safety. Here, we present methods used to (1) screen for tLST genes by multiplex PCR and (2) screen and isolate XHR E. coli from meat sources. The mode of heat exposure affects the outcome of XHR testing. Hence, the protocols were optimized to achieve maximum agreement between the tLST genotype and the XHR phenotype.

Screening of Antibiotic and Virulence Genes from Whole Genome Sequenced Cronobacter sakazakii Isolated from Food and Milk-Producing Environments

The objective of this study was to use whole-genome sequencing (WGS) to screen for genes encoding for antibiotic resistance, fitness and virulence in Cronobacter sakazakii strains that had been isolated from food and powdered-milk-producing environments. Virulence (VGs) and antibiotic-resistance genes (ARGs) were detected with the Comprehensive Antibiotic Resistance Database (CARD) platform, ResFinder and PlasmidFinder tools. Susceptibility testing was performed using disk diffusion. Fifteen presumptive strains of Cronobacter spp. were identified by MALDI-TOF MS and ribosomal-MLST. Nine C. sakazakii strains were found in the meningitic pathovar ST4: two were ST83 and one was ST1. The C. sakazakii ST4 strains were further distinguished using core genome MLST based on 3678 loci. Almost all (93%) strains were resistant to cephalotin and 33% were resistant to ampicillin. In addition, 20 ARGs, mainly involved in regulatory and efflux antibiotics, were detected. Ninety-nine VGs were detected that encoded for OmpA, siderophores and genes involved in metabolism and stress. The IncFIB (pCTU3) plasmid was detected, and the prevalent mobile genetic elements (MGEs) were ISEsa1, ISEc52 and ISEhe3. The C. sakazakii isolates analyzed in this study harbored ARGs and VGs, which could have contributed to their persistence in powdered-milk-producing environments, and increase the risk of infection in susceptible population groups.

Distribution of Extremely Heat-Resistant Escherichia coli in the Beef Production and Processing Continuum

Understanding the dynamics of stress-resistant Escherichia coli (E. coli) across the meat production and processing continuum is important for tracking sources of such microbes and devising effective modes of control. The Locus of Heat Resistance (LHR) is a ∼14-19 Kb genetic element imparting extreme heat resistance (XHR) in Enterobacteriaceae. It has been hypothesized that thermal and antimicrobial interventions applied during meat processing may select for LHR⁺E. coli. Thus, our goal was to study the prevalence and molecular biology of LHR⁺E. coli among lots of beef cattle (n = 3) from production through processing. Two hundred thirty-two generic E. coli isolated from the same animals through seven stages of the beef processing continuum (cattle in feedyards to packaged strip loins) were examined. LHR⁺E. coli were rare (0.6%; 1 of 180) among the early stages of the beef continuum (feces and hides at feedlot, feces and hides at harvest, and preevisceration carcasses), whereas the prevalence of LHR⁺E. coli on final carcasses and strip loins was remarkably higher. Half (14 of 28) of the final carcass E. coli possessed the LHR, while 79.2% (19 of 24) of the strip loin E. coli did. Eighty-five percent (29 of 34) of the LHR⁺E. coli presented with the XHR phenotype. The selection or enrichment of LHR⁺E. coli from harvest steps to the final products appeared unlikely as the LHR⁺E. coli isolates were effectively controlled by antimicrobial interventions typically used during beef processing. Further, whole-genome sequencing of the isolates suggested LHR⁺E. coli are persisting in the chilled processing environment and that horizontal LHR transfer among E. coli isolates may take place.

Genomic and Phenotypic Analysis of Heat and Sanitizer Resistance in Escherichia coli from Beef in Relation to the Locus of Heat Resistance

The locus of heat resistance (LHR) can confer heat resistance to Escherichia coli to various extents. This study investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR recovered from beef by direct plating or from enrichment broth at 42°C. LHR-positive E. coli isolates (n = 24) were subjected to whole-genome sequencing by short and long reads. LHR-negative isolates (n = 18) from equivalent sources as LHR-positive isolates were short-read sequenced. All isolates were assessed for decimal reduction time at 60°C (D_60°C) and susceptibility to the sanitizers E-SAN and Perox-E. Selected isolates were evaluated for growth at 42°C. The LHR-positive and -negative isolates were well separated on the core genome tree, with 22/24 positive isolates clustering into three clades. Isolates within clade 1 and 2, despite their different D_60°C values, were clonal, as determined by subtyping (multilocus sequence typing [MLST], core genome MLST, and serotyping). Isolates within each clade are of one serotype. The LHR-negative isolates were genetically diverse. The LHR-positive isolates had a larger (P < 0.001) median genome size by 0.3 Mbp (5.0 versus 4.7 Mbp) and overrepresentation of genes related to plasmid maintenance, stress response, and cryptic prophages but underrepresentation of genes involved in epithelial attachment and virulence. All LHR-positive isolates harbored a chromosomal copy of LHR, and all clade 2 isolates had an additional partial copy of LHR on conjugative plasmids. The growth rates at 42°C were 0.71 ± 0.02 and 0.65 ± 0.02 log(OD) h^-1 for LHR-positive and -negative isolates, respectively. No meaningful difference in sanitizer susceptibility was noted between LHR-positive and -negative isolates. IMPORTANCE Resistant bacteria are serious food safety and public health concerns. Heat resistance conferred by the LHR varies largely among different strains of E. coli. The findings in this study show that genomic background and composition of LHR, in addition to the presence of LHR, play an important role in the degree of heat resistance in E. coli and that strains with certain genetic backgrounds are more likely to acquire and maintain the LHR. Also, caution should be exercised when recovering E. coli at elevated temperatures, as the presence of LHR may confer growth advantages to some strains. Interestingly, the LHR-harboring strains seem to have evolved further from their primary animal host to adapt to their secondary habitat, as reflected by fewer genes involved in virulence and epithelial attachment. The phylogenetic relationships among the isolates point toward multiple mechanisms for acquisition of LHR by E. coli, likely prior to its being deposited on meat.

Locus of Heat Resistance (LHR) in Meat-Borne Escherichia coli: Screening and Genetic Characterization

Microbial resistance to processing treatments poses a food safety concern, as treatment tolerant pathogens can emerge. Occasional foodborne outbreaks caused by pathogenic Escherichia coli have led to human and economic losses. Therefore, this study screened for the extreme heat resistance (XHR) phenotype as well as one known genetic marker, the locus of heat resistance (LHR), in 4,123 E. coli isolates from diverse meat animals at different processing stages. The prevalences of XHR and LHR among the meat-borne E. coli were found to be 10.3% and 11.4%, respectively, with 19% agreement between the two. Finished meat products showed the highest LHR prevalence (24.3%) compared to other processing stages (0 to 0.6%). None of the LHR⁺ E. coli in this study would be considered pathogens based on screening for virulence genes. Four high-quality genomes were generated by whole-genome sequencing of representative LHR⁺ isolates. Nine horizontally acquired LHRs were identified and characterized, four plasmid-borne and five chromosomal. Nine newly identified LHRs belong to ClpK1 LHR or ClpK2 LHR variants sharing 61 to 68% nucleotide sequence identity, while one LHR appears to be a hybrid. Our observations suggest positive correlation between the number of LHR regions present in isolates and the extent of heat resistance. The isolate exhibiting the highest degree of heat resistance possessed four LHRs belonging to three different variant groups. Maintenance of as many as four LHRs in a single genome emphasizes the benefits of the LHR in bacterial physiology and stress response.IMPORTANCE Currently, a "multiple-hurdle" approach based on a combination of different antimicrobial interventions, including heat, is being utilized during meat processing to control the burden of spoilage and pathogenic bacteria. Our recent study (M. Guragain, G. E. Smith, D. A. King, and J. M. Bosilevac, J Food Prot 83:1438-1443, 2020, https://doi.org/10.4315/JFP-20-103) suggests that U.S. beef cattle harbor Escherichia coli that possess the locus of heat resistance (LHR). LHR seemingly contributes to the global stress tolerance in bacteria and hence poses a food safety concern. Therefore, it is important to understand the distribution of the LHRs among meat-borne bacteria identified at different stages of different meat processing systems. Complete genome sequencing and comparative analysis of selected heat-resistant bacteria provide a clearer understanding of stress and heat resistance mechanisms. Further, sequencing data may offer a platform to gain further insights into the genetic background that provides optimal bacterial tolerance against heat and other processing treatments.

Electrically-responsive antimicrobial coatings based on a tetracycline-loaded poly(3,4-ethylenedioxythiophene) matrix

The growth of bacteria and the formation of complex bacterial structures on biomedical devices is a major challenge in modern medicine. The aim of this study was to develop a biocompatible, conducting and antibacterial polymer coating applicable in biomedical engineering. Since conjugated polymers have recently aroused strong interest as controlled delivery systems for biologically active compounds, we decided to employ a poly(3,4-ethylenedioxythiophene) (PEDOT) matrix to immobilize a powerful, first-line antibiotic: tetracycline (Tc). Drug immobilization was carried out simultaneously with the electrochemical polymerization process, allowing to obtain a polymer coating with good electrochemical behaviour (charge storage capacity of 19.15 ± 6.09 mC/cm²) and high drug loading capacity (194.7 ± 56.2 μg/cm²). Biological activity of PEDOT/Tc matrix was compared with PEDOT matrix and a bare Pt surface against a model Gram-negative bacteria strain of Escherichia coli with the use of LIVE/DEAD assay and SEM microscopy. Finally, PEDOT/Tc was shown to serve as a robust electroactive coating exhibiting antibacterial activity.

Basic mechanism of the autonomous ClpG disaggregase

Bacterial survival during lethal heat stress relies on the cellular ability to reactivate aggregated proteins. This activity is typically executed by the canonical 70-kDa heat shock protein (Hsp70)–ClpB bichaperone disaggregase, which is most widespread in bacteria. The ClpB disaggregase is a member of the ATPase associated with diverse cellular activities protein family and exhibits an ATP-driven threading activity. Substrate binding and stimulation of ATP hydrolysis depends on the Hsp70 partner, which initiates the disaggregation reaction. Recently elevated heat resistance in gamma-proteobacterial species was shown to be mediated by the ATPase associated with diverse cellular activities protein ClpG as an alternative disaggregase. Pseudomonas aeruginosa ClpG functions autonomously and does not cooperate with Hsp70 for substrate binding, enhanced ATPase activity, and disaggregation. With the underlying molecular basis largely unknown, the fundamental differences in ClpG- and ClpB-dependent disaggregation are reflected by the presence of sequence alterations and additional ClpG-specific domains. By analyzing the effects of mutants lacking ClpG-specific domains and harboring mutations in conserved motifs implicated in ATP hydrolysis and substrate threading, we show that the N-terminal, ClpG-specific N1 domain generally mediates protein aggregate binding as the molecular basis of autonomous disaggregation activity. Peptide substrate binding strongly stimulates ClpG ATPase activity by overriding repression by the N-terminal N1 and N2 domains. High ATPase activity requires two functional nucleotide binding domains and drives substrate threading which ultimately extracts polypeptides from the aggregate. ClpG ATPase and disaggregation activity is thereby directly controlled by substrate availability.

Prevalence of Extreme Heat-Resistant Gram-Negative Bacteria Carried by U.S. Cattle at Harvest

ABSTRACT

Prevalence of heat-resistant bacteria in beef poses a potential problem as thermal interventions are routinely used in beef processing to control contamination. Despite extreme heat-resistant (XHR) Escherichia coli having been isolated from a ground beef processing plant, there has not been a study to assess the prevalence of XHR E. coli among types of cattle. Therefore, this study used a screening assay for XHR gram-negative bacteria and its molecular determinant, the locus of heat resistance (LHR), on feces collected from U.S. cattle. Fecal samples were collected from fed (n = 538), cull dairy (n = 425), and cull beef (n = 475) cattle at nine regional beef processing plants located across the United States. Among the 1,438 cattle sampled from northern (n = 288), southern (n = 288), eastern (n = 287), western (n = 287), and central (n = 288) regions of the United States, 91 (6.3%) cattle showed presence of XHR bacteria, as evident by growth in MacConkey broth following heat treatment of 80°C for 15 min, in their feces. Heat-resistant bacteria (n = 140) were isolated from the 91 fecal samples. Prevalence of XHR bacteria was highest (11%) in cattle from the northern region. Ninety percent of the XHR isolates were identified as E. coli. Multiplex PCR of all 1,438 fecal samples showed that the LHR was absent in 40.7% of samples and intact in 18.7% of samples. Despite the higher prevalence of intact LHR from PCR analysis, only 11 samples (0.8%) were confirmed to contain bacteria with an intact LHR. The LHR was absent in 91% of XHR bacteria, and only 7.9% of XHR bacteria had intact LHR, suggesting a novel mechanism of heat resistance. By developing and using the screening assays, we established the prevalence of XHR bacteria (6.3%) and LHR+ bacteria (0.8%) in U.S. beef cattle.

HIGHLIGHTS

Are Antimicrobial Interventions Associated with Heat-Resistant Escherichia coli on Meat?

Decontamination practices, which often involve thermal treatments, are routinely performed in beef packing plants and have generally improved the safety of meat in North America. We investigated whether Escherichia coli in the beef production chain is becoming more heat resistant due to those treatments. Cattle isolates (n = 750) included seven serogroups (O157, O103, O111, O121, O145, O26, and O45) which were collected between 2002 and 2017. Beef plant isolates (n = 700) from carcasses, fabrication equipment, and beef products were included. Heat resistance was determined in Luria-Bertani broth at 60°C and by PCR screening for the locus of heat resistance (LHR). The decimal reduction for E. coli at 60°C (D _60ºC values) ranged from 0 to 7.54 min, with 97.2% of the values being <2 min. The prevalence of E. coli with D _60ºC values of >2 min was not significantly different (P > 0.05) among cattle and meat plant isolates. E. coli from equipment before sanitation (median, 1.03 min) was more heat resistant than that after sanitation (median, 0.9 min). No significant difference in D _60ºC values was observed among E. coli isolates from different years, from carcasses before and after antimicrobial interventions, or from before and during carcass chilling. Of all isolates, 1.97% harbored LHR, and the LHR-positive isolates had greater median D _60ºC values than the LHR-negative isolates (3.25 versus 0.96 min). No increase in heat resistance in E. coli was observed along the beef production chain or with time.IMPORTANCE The implementation of multiple hurdles in the beef production chain has resulted in substantial improvement in the microbial safety of beef in Canada. In this study, we characterized a large number of Escherichia coli isolates (n = 1,450) from various sources/stages of beef processing to determine whether the commonly used antimicrobial interventions would give rise to heat-resistant E. coli on meat, which in turn may require alternatives to the current control of pathogens and/or modifications to the current cooking recommendations for meat. The findings show that the degree and rate of heat resistance in E. coli did not increase along the production chain or with time. This furthers our understanding of man-made ecological niches that are required for the development of heat resistance in E. coli.

Characterization of Escherichia coli possessing the locus of heat resistance isolated from human cases of acute gastroenteritis

The purpose of this study was to identify Escherichia coli isolates obtained from patients experiencing acute gastroenteritis that possess the locus of heat resistance (LHR) and characterize their heat resistance upon exposure to temperatures of 60 °C and 71 °C. From a collection of 613 clinical E. coli strains, 3 heat resistant E. coli isolates were identified. Two of the 3 isolates were stx₁ positive; no isolates possessed stx₂ as determined by qPCR. D₆₀-values of heat resistant isolates all exceeded 10.20 min with one isolate's D₆₀-values ranging from 20.46 to 72.47 min. The presence of 4% additional NaCl significantly increased D₆₀-values of 2 clinical isolates. Cell reductions of heat resistant isolates in ground beef patties grilled to 60 °C and 71 °C remained above 2.8 and 4.9 log CFU/mL, respectively, compared to reductions of 6.1 log CFU/mL and greater in heat sensitive E. coli. Constitutive expression of novel Clp protease ClpK, encoded on open reading frame 3 of the LHR, was identified in all heat resistant isolates by SDS-PAGE and peptide mass fingerprinting. This data is the first to report heat resistant E. coli possessing the LHR involved in clinical infection, highlighting the potential threat of heat resistant enteric pathogens on food safety.

ClpG Provides Increased Heat Resistance by Acting as Superior Disaggregase

Elevation of temperature within and above the physiological limit causes the unfolding and aggregation of cellular proteins, which can ultimately lead to cell death. Bacteria are therefore equipped with Hsp100 disaggregation machines that revert the aggregation process and reactivate proteins otherwise lost by aggregation. In Gram-negative bacteria, two disaggregation systems have been described: the widespread ClpB disaggregase, which requires cooperation with an Hsp70 chaperone, and the standalone ClpG disaggregase. ClpG co-exists with ClpB in selected bacteria and provides superior heat resistance. Here, we compared the activities of both disaggregases towards diverse model substrates aggregated in vitro and in vivo at different temperatures. We show that ClpG exhibits robust activity towards all disordered aggregates, whereas ClpB acts poorly on the protein aggregates formed at very high temperatures. Extreme temperatures are expected not only to cause extended protein unfolding, but also to result in an accelerated formation of protein aggregates with potentially altered chemical and physical parameters, including increased stability. We show that ClpG exerts higher threading forces as compared to ClpB, likely enabling ClpG to process “tight” aggregates formed during severe heat stress. This defines ClpG as a more powerful disaggregase and mechanistically explains how ClpG provides increased heat resistance.

Turn Up the Heat-Food and Clinical Escherichia coli Isolates Feature Two Transferrable Loci of Heat Resistance

Heat treatment is a widely used process to reduce bacterial loads in the food industry or to decontaminate surfaces, e.g., in hospital settings. However, there are situations where lower temperatures must be employed, for instance in case of food production such as raw milk cheese or for decontamination of medical devices such as thermo-labile flexible endoscopes. A recently identified locus of heat resistance (LHR) has been shown to be present in and confer heat resistance to a variety of Enterobacteriaceae, including Escherichia coli isolates from food production settings and clinical ESBL-producing E. coli isolates. Here, we describe the presence of two distinct LHR variants within a particularly heat resistant E. coli raw milk cheese isolate. We demonstrate for the first time in this species the presence of one of these LHRs on a plasmid, designated pFAM21805, also encoding type 3 fimbriae and three bacteriocins and corresponding self-immunity proteins. The plasmid was highly transferable to other E. coli strains, including Shiga-toxin-producing strains, and conferred LHR-dependent heat resistance as well as type 3 fimbriae-dependent biofilm formation capabilities. Selection for and acquisition of this “survival” plasmid by pathogenic organisms, e.g., in food production environments, may pose great concern and emphasizes the need to screen for the presence of LHR genes in isolates.